Browsing Center for Advanced Genomic Technology by Title

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Browsing Center for Advanced Genomic Technology by Title

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  • Phylogenetic Detection of Conserved Gene Clusters in Microbial Genomes
    Zheng, Yu; Anton, Brian P; Roberts, Richard J; Kasif, Simon (BioMed Central, 2005-10-3)
    BACKGROUND. Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional ...
  • Portraits of Breast Cancer Progression
    Dalgin, Gul S; Alexe, Gabriela; Scanfeld, Daniel; Tamayo, Pablo; Mesirov, Jill P; Ganesan, Shridar; DeLisi, Charles; Bhanot, Gyan (BioMed Central, 2007-8-6)
    BACKGROUND. Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based ...
  • A Predictive Phosphorylation Signature of Lung Cancer
    Wu, Chang-Jiun; Cai, Tianxi; Rikova, Klarisa; Merberg, David; Kasif, Simon; Steffen, Martin (Public Library of Science, 2009-11-25)
    BACKGROUND. Aberrant activation of signaling pathways drives many of the fundamental biological processes that accompany tumor initiation and progression. Inappropriate phosphorylation of intermediates in these signaling ...
  • Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical Clustering
    Dotan-Cohen, Dikla; Kasif, Simon; Melkman, Avraham A. (Oxford University Press, 2009-6-3)
    Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological ...
  • VisANT 3.0: New Modules for Pathway Visualization, Editing, Prediction and Construction
    Hu, Zhenjun; Ng, David M.; Yamada, Takuji; Chen, Chunnuan; Kawashima, Shuichi; Mellor, Joe; Linghu, Bolan; Kanehisa, Minoru; Stuart, Joshua M.; DeLisi, Charles (Oxford University Press, 2007-07)
    With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) ...
  • VisANT 3.5: Multi-Scale Network Visualization, Analysis and Inference Based on the Gene Ontology
    Hu, Zhenjun; Hung, Jui-Hung; Wang, Yan; Chang, Yi-Chien; Huang, Chia-Ling; Huyck, Matt; DeLisi, Charles (2009-7-1)
    Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on ...

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